Related papers: Computer Simulation of Biological Processes at the…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown…
Bio-hybrid systems---close couplings of natural organisms with technology---are high potential and still underexplored. In existing work, robots have mostly influenced group behaviors of animals. We explore the possibilities of mixing…
Recent empirical work has shown that human children are adept at learning and reasoning with probabilities. Here, we model a recent experiment investigating the development of school-age children's non-symbolic probability reasoning ability…
These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing Machines that we introduced in a previous article. The use of Turing Machines allows for very simple mechanisms of code growth and code…
Machine Learning tools are nowadays widely applied extensively to the prediction of the properties of molecular materials, using datasets extracted from high-throughput computational models. In several cases of scientific and technological…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
The formation and development of the human person is most influenced by the environment in which it lives, studies, works. Therefore, the problem of the creation of such a high-tech information and communication educational and scientific…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
A growing number of universities worldwide use various forms of online and blended learning as part of their academic curricula. Furthermore, the recent changes caused by the COVID-19 pandemic have led to a drastic increase in importance…
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific…
Formal modelling provides a toolkit for understanding cultural dynamics, from individual decisions to recurring patterns of change. This chapter explains what models are and why they matter. Using a precise, shared language, they aid…